I think you have a found a supercell and dont really need to run any MR
program to find the solution - just reposition the molecule
Your P422 point group cell is
126.514 126.514 76.766 90.00 90.00 90.00
Your I422 point group cellis:
180.096 180.096 152.530 90.00 90.00 90.00
Note c is doubled
a = b = a_P422 * sqrt(2)
And you have a large off origin peak in the Patterson ( that is the
meaning of the "As shown in"Analyse Data for MR", the first peak is 100
and second is 68.92" message
You dont give the coordinates but I bet it is related to the supercell
ness ( P42 22 is a subgroup of I422)
By the way where is that peak?
Si I suspect the structures are the same and you have either integrated
in too large cell for the I422 version,or missed some data in the P4222;
I suggest you take your P42 22 solution. rotate the coordinates by 45
degrees to get to the I422 axes
pdbset xyzin P42222.pdb xyzout I422A.pdb
cell 180.096 180.096 152.530 90.00 90.00 90.00
rotate euler 0 0 45
end
Then generate the translated molecule
pdbset xyzin I422A.pdb xyzout I422B.pdb
shift frac x y z (taken for the off origin translation from above)
end
Combine the two pdbs I422A.pdb and I422B.pdb
(Edit them to make sure there is only one header and end card )
Try that as a solution.
Eleanor
Actually, another thing could be going on as well. You show a large
off-origin peak in the Patterson in I422 so you may have
pseudotranslation going on and you processed in the supercell. You could
probably try to reindex choosing fewer spots and get your P422 cell. I
am sure there is some law that would convert your P422 cell to I422 (or
vice versa), but I don't know it off the top of my head. That way you
could just look at your cell lengths and see if this is possible. Its
probably the same crystal form, except this crystal has PTS.
Jon
Chao Quan wrote:
Dear CCP4 community:
I am a beginner to crystallography and therefore my apologies if this
question is too simple.
Basically we obtained several crystal forms of the same molecule,
which is a hetero-
trimer containing protein A(18kD), protein B(16kD) and a RNA
segment(40nt or about 15kD).
We have solved the structure of one crystal form(form_1); its
information is as follows:
space group = P 42 22;
unit cell = 126.514 126.514 76.766 90.00 90.00 90.00
resolution = 2.7A;
Rwork = 0.25, Rfree = 0.265;
solvent content = 60%;
Number of molecules per Asymmetric Unit = 1;
Data redundancy = 5;
Data Completeness = 94%;
I am now trying to solve the structure of form_2 crystal using
molecular replacement. So far the information I know about form_2 is
as follows:
space group = I 422 or I 41 22;
unit cell = 180.096 180.096 152.530 90.00 90.00 90.00
(unit cell is about 4 times the size of form_1)
resolution = 3.3A; (which is low)
Number of molecules per Asymmetric Unit = 2 or 3;
Data redundancy = 4;
Data Completeness = 92%;
There is no twinning(as shown by Sfcheck);
As shown in"Analyse Data for MR", the first peak is 100 and second is
68.92; I am not sure if this indicates translation in a Asymmetric Unit;
The problem is, I can not get a good solution by MR using Phaser (both
I422 and I4122 are tried). When I searched for 3 molecules per
Asymmetric Unit, Phaser did not give solutions at all.
When I used 2/ASU instead, I was able to get some solutions, with
typical statistics as follows:
RFZ=14, TFZ=35.9, PAK=0, LLG=1036; However, these solutions had high R
values(like Rwork=0.59 and Rfree=0.58), which indicated that they are
not solutions at all. Still, I tried refinement using refmac5, but R
values did not go down even after 50 rounds; sometimes they even
increased after refinement.
Besides, the RMS values bond length, bond angle and chiral center were
all 0 as show by refmac5.
I tried limiting resolution range to 15-4A in Phaser, which did not
help either.
Now I am completely stuck. Could anyone give me some advice? I know
this situation is very strange, because I am using the SAME molecule
for MR but can not can a solution.
Thanks a lot,
P.S. 1) Both form_1 and form_2 crystals were grown using
Selenomethionine-containing samples. There are 3 Sel_Met in protein A
and 1 in protein B. 2) A 10-aa internal segment of protein B is
missing in the solved structure, which may indicate high flexibility.
Chao
